[BioC] Limma:Single Channel Normalization for two color Arrays

Binita Dutta binita.dutta at vib.be
Wed Jun 30 10:56:37 CEST 2004

Dear All,

I have done single channel normalization for 8 arrays.

   Sl.No. Slide.Name        Cy5        Cy3
1      1 2003110429  J  2 0min      J2 30min
2      2 2003110430  J2 0min        J3 0min
3      3 2003110431  J2 30min      J3 30min
4      4 2003110432  J3 0min        J3 30min
5      5 2003110433  J2 30min      J2 0min
6      6 2003110434  J3 0min        J2 0min
7      7 2003110435  J3 30min      J2 30min
8      8 2003110436  J3 30min      J3 0min

Can we used the normalized intensities (red and green channel) instead of 
normalized MA, to determine differentially expressed genes with design 
matrix  similar to what we use for analysis for Affymetrix data.

I have been unable to export normalized Green and Red channel intensities.

However, when i use following commands, I get M and A values.

  write.table(MA.p$A,file="h:\\r\\Exp200\\single channel nor A.txt", append 
= FALSE, sep = "\t", eol="\n", na="NA", dec="")
  write.table(MA.p$M,file="h:\\r\\Exp200\\single channel nor M.txt", append 
= FALSE, sep = "\t", eol="\n", na="NA", dec="").

Please suggest me how can i export normalized red and green channel intesities.

I have other experiments to analyse and would like to use single channel 

Thanks in advance



Binita Dutta, PhD
MicroArray Facility(MAF)
UZ Gasthuisberg
Onderwijs en Navorsing
Herestraat 49
3000 Leuven

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